Shield use and armor layers will not make a difference on whether or not you actually get hit... It just determines if you get hurt from it at all.
So every time you get an arrow that glances off your armor or is deflected by your shield, you were "hit" by an arrow.
In general, archers will mean your death. I cripple the damage done by various projectiles, and even with that I find myself getting obliterated by a single arrow or bolt. They can fire very quickly, have very good accuracy (in general), and can kill you in one hit.
There are three ways of somewhat-effectively avoiding death by projectile. Shields, stealth, and wrestling.
Shields, with very high skill (and a few extra shields strapped on, of course), can deflect most arrows coming at you. Stealth can get you past all arrows and all notice, but only if you don't get caught. Also, don't try to backstab an archer... They get the first shot, regardless of how you approach the problem.
And then there's wrestling... If you manage to get exceptionally high wrestling skill (along with a fair amount of agility) you can pull a Neo and simply jump away from all projectiles making their way towards you. Well, almost all of them.
Oh, and if you find yourself right next to a ranged opponent (they will continue firing at you in melee, which is bad news for you), try this handy little trick... Using a free grasp (limbs don't work for this), grab their quiver. Once you've got it, go into your inventory and you will find the quiver highlighted as a wrestled object (I.E., you'd have to grab it away from them before you can do stuff with it). However, the arrows inside the quiver are considered yours. Simply [d]rop the arrows, and he'll have no more ammo. You may then release the quiver.
You can do this to sleeping guards without waking them up, by the way.